SMTL ID : 6kqp.1

NSD1 SET domain in complex with SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 19 residues within 4Å: Chain A: R.89, G.90, W.91, T.131, N.132, F.133, Y.134, R.154, F.155, M.156, N.157, H.158, Y.195, N.202, V.206, C.207, K.208, C.209, L.218 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.91, A:T.131, A:N.132, A:F.133, A:F.133, A:N.157, A:H.158, A:H.158, A:N.202, A:K.208 SAM.5: 19 residues within 4Å: Chain B: R.89, G.90, W.91, T.131, N.132, F.133, Y.134, R.154, F.155, M.156, N.157, H.158, Y.195, N.202, V.206, C.207, K.208, C.209, L.218 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:W.91, B:T.131, B:N.132, B:F.133, B:F.133, B:Y.134, B:N.157, B:H.158, B:H.158, B:N.202, B:K.208

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.160, C.207, C.209, C.214 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.160, A:C.207, A:C.209, A:C.214 ZN.3: 5 residues within 4Å: Chain A: C.42, C.57, C.62, C.68 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.42, A:C.57, A:C.62, A:C.68 ZN.4: 6 residues within 4Å: Chain A: C.32, C.34, C.42, C.48, C.57 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.32, A:C.34, A:C.42, A:C.48 ZN.6: 4 residues within 4Å: Chain B: C.160, C.207, C.209, C.214 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.160, B:C.207, B:C.209, B:C.214 ZN.7: 5 residues within 4Å: Chain B: C.42, C.57, C.62, C.68 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.42, B:C.57, B:C.62, B:C.68 ZN.8: 6 residues within 4Å: Chain B: C.32, C.34, C.42, C.48, C.57 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.32, B:C.34, B:C.42, B:C.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, H. et al., Covalent inhibition of NSD1 histone methyltransferase. Nat.Chem.Biol. (2020)

Release Date

2020-09-02

Peptides

Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific